Molecular studies of some micro-organisms are hampered by the difficulty of obtaining sufficient amounts of nucleic acids. A cloning strategy based on PCR has therefore been used to clone the eburicol 14α-demethylase (CYP51) gene of the obligate fungus Erysiphe graminis f. sp. hordei (Egh) using minute amounts of genomic DNA. The CYP51 gene encodes the enzymatic target of a major group of fungicides. Sequencing CYP51 from different Egh isolates revealed the occurrence of two alleles for this gene. An allele-specific PCR assay was developed to detect each CYP51 allele.

The Saccharomyces cerevisiae ngs1-1 mutant was previously identified by its enhanced sensitivity to simple DNA-alkylating agents such as methyl methanesulfonate but not to UV. Molecular cloning and sequencing of NGS1 as a putative DNA-alkylation repair gene revealed that it is identical to MRE11, a gene that is involved in DNA recombinational repair. In order to investigate functional domains of the Mre11 protein, nucleotide-sequence alterations of a number of mre11 mutant alleles, including ngs1-1, mre11-1 (ts), mre11-2, mre11-3 and mre11-58, were determined. Most of these mutations map to the N-terminus of Mre11, emphasizing the importance of this highly conserved domain. The ngs1-1 and mre11-3 mutants carry nonsense mutations resulting in truncated proteins. Missense mutations were found in mre11-1 (ts), mre11-2 and mre11-58, of which mre11-2 and mre11-58 mapped to the conserved phosphoesterase domains, indicating the involvement of these motifs in the formation and/or processing of DNA double-strand breaks. Finally, mitotic-recombination assays show that the mre11Δ mutation enhances inter-chromosomal recombination but decreases the intra-chromosomal deletion frequency. In addition, MRE11 appears to play different roles during spontaneous and alkylation-induced homologous mitotic recombination.

The nitrate reductase gene (NIA1) of the phytopathogenic fungus Stagonospora (Septoria) nodorum has been cloned from a cosmid library by homologous hybridisation with a PCR-generated probe. A 6.7-kb fragment carrying the NIA1 gene was subcloned and partially characterised by restriction mapping. Sequencing of the gene indicated a high degree of homology, both at the nucleotide and amino-acid levels, with nitrate reductase genes of other filamentous fungi. Furthermore, consensus regulatory signals thought to be involved in the control of nitrogen metabolism are present in the 5′ flanking region. The cloned NIA1 gene has been used to develop a gene-transfer system based on nitrate assimilation. Stable nia1 mutants of S. nodorum defective in nitrate reductase were isolated by virtue of their resistance to chlorate. These were transformed back to nitrate utilisation with the wild-type S. nodorum NIA1 gene. Southern analyses revealed that transformation occurred as a result of the integration of transforming DNA into the fungal genome; in all cases examined, integration was targeted to the homologous sequence.

The biosynthesis of starch in red algae occurs in the cytosol, in contrast to green plants where it takes place in the plastid. We have cloned a nuclear gene from the red alga Gracilaria gracilis that encodes a homolog of starch-branching enzymes (SBEs); this gene, which is apparently intron-free, was designated as GgSBE1. A potential TATA box, CAAT boxes, and other potential regulatory elements were observed in its 5′ flanking region. The encoded 766-aa peptide shares significant sequence similarity with SBEs from green plants (at least 40%), and with glycogen-branching enzymes (GBEs) from human (46%) and Saccharomyces cerevisiae (45%). Southern-hybridization analysis indicates that the gene is single-copy, although weaker signals suggest that related genes exist in the genome of G. gracilis. Phylogenetic analyses indicate that GgSBE1 groups within the eukaryote branching enzymes (BEs) and not with eubacterial GBEs, suggesting that its gene has not been derived directly from an endosymbiotic cyanobacterium, but instead is ancestrally eukaryotic.

The sequences of the rps4 and rps10 genes encoding the Dictyostelium discoideum homologues of the basic ribosomal proteins S4 and S10 were determined from cDNA and genomic DNA clones. They are expressed respectively as 266 and 153 amino-acid-long proteins. In both cases, the N-terminal methionine is cleaved in the mature proteins. S4 contains two putative nuclear targeting signals and displays a strong overall identity (around 60%) to eukaryotic S4 homologues. The rps10 gene harbours a 314-bp intron located close to its 5′-coding end. The overall identity between D. discoideum S10 and eukaryotic homologues is around 38% and rises to 53% in the N-terminal domain. Southern blots suggest that both S4 and S10 are encoded by single genes that are regulated during development. The corresponding mRNAs decrease sharply after 8 h of differentiation.

A Neurospora crassa gene encoding a product with homology to the Saccharomyces cerevisiae Rad1 nucleotide excision repair (NER) protein was isolated by degenerate PCR. The predicted protein consists of 892 amino acids with a molecular weight of 100.4 kDa, and 32–37% identity to the XPF/ERCC4 protein family. The homolog was mapped to the left arm of linkage group I, the location of the mus-38 gene. Subsequently, gene inactivation and complementation studies identified the RAD1 homolog as mus-38. Immunological assays showed that the mus-18 (UV-specific endonuclease) and mus-38 strains have partial and normal UV-damage excision activities, respectively, but removal of thymine dimers and TC (6-4) photoproducts is abolished in the mus-18 mus-38 double mutant. The double mutant also was synergistically more sensitive to UV than either single mutant. The data suggest that mus-38 may participate in a different NER pathway from that involving the mus-18 gene.

GPD regulatory sequences were used to express a phleomycin resistance gene (Sh ble) in Schizophyllum commune, resulting in high numbers of phleomycin-resistant transformants. Attempts to express heterologous genes coding for hygromycin B phosphotransferase (hph), aminoglycoside phosphotransferase (apt), β-glucuronidase (uidA) and β-galactosidase (lacZ) using the same regulatory sequences were not successful and no mRNA could be detected. Cloning the hph and uidA genes in an internally deleted GPD gene resulted in truncated transcripts which ended within the 5′-parts of the heterologous genes. Cloning of the same genes as transcriptional fusions downstream from the Sh ble gene also resulted in truncated transcripts ending in the 5′-parts of these heterologous genes. It is suggested that AT-rich sequences in heterologous genes might be involved in generating these truncated transcripts, thereby preventing expression in S. commune.

The gene coding for copalyl diphosphate synthase (CPS), which represents the first gene of the gibberellin pathway, was isolated from the rice pathogen Gibberella fujikuroi. This fungus is used commercially for the production of gibberellic acid and related gibberellins. CPS is a terpene cyclase which catalyzes the first specific step of the gibberellin (GA) pathway as it branches off from the general isoprenoid (biosynthetic) pathway at geranylgeranyl disphosphate (GGDP). A cDNA fragment of the cps gene from the fungus G. fujikuroi was amplified by RT-PCR using oligonucleotides based on amino-acid sequences which were conserved between the plant CPSs and the bifunctional CPS/KS of the fungus Phaeosphaeria sp. L487. A 588-bp fragment obtained with nested PCR was used to isolate the corresponding genomic clone of the cps gene from the wild-type λ-library. This gene consists of three exons and two introns. The three exons are 2877 bp long and encode 959 amino-acid residues. The protein shares 48% identity with the bifunctional Phaeosphaeria sp. L487 FCPS and between 16% and 18% identity to the corresponding plant CPSs. Expression of the G. fujikuroi cps gene is strongly enhanced under conditions optimized for gibberellin biosynthesis and is reduced when high amounts of ammonium are present in the medium. Gene disruption, followed by gibberellin assays and Southern-blot analysis of the transformants, demonstrated clearly that the cloned gene has the expected function in the biosynthesis of fungal gibberellins.

By a genomic comparison of two sibling yeasts, Saccharomyces bayanus and S. cerevisiae, we previously demonstrated that chromosomes II and IV of S. cerevisiae were rearranged into chromosomes 12 and 14 of S. bayanus or vice versa. In the present study we have delimited the translocation break sites in chromosomes II and IV by Southern hybridization using DNA fragments of S. cerevisiae cosmid clones as probes. The results suggest that the reciprocal translocation of chromosomes II and IV had occurred at duplicated RPL2 loci. Furthermore, the translocation sites in S. bayanus were confirmed by the cloning and sequence analysis of the regions flanking RPL2 loci. Several genes in the regions flanking the RPL2 loci were present in the order expected for a translocation at these loci between the two species. These results indicated that the reciprocal translocation between chromosomes II and IV was generated by homologous recombination at duplicated RPL2 loci on the two chromosomes. Therefore, we propose that duplicated genes or duplicated regions play an important role in altering genomic organization during the speciation of S. bayanus and S. cerevisiae.

Conservation of telomeric DNA repeat sequences has been found across evolutionarily diverse eukaryotes. Here we report on a marked telomeric sequence diversity within the budding yeast genus Saccharomyces. Cloning and sequencing of telomeric repeat units from S. castellii, S. dairensis, S. exiguus and S. kluyveri showed a length variation between 8 and 26 bp, as well as a distinct variation in the degree of homogeneity, among the species. In S. castellii and S. dairensis, TCTGGGTG constituted a majority of the telomeric repeat units. However, the character of the variant repeats differed: in S. castellii the major class of variant repeats contained additional TG dinucleotides per repeat unit, [TCTGGGTG(TG)1–3], whereas in S. dairensis the major variant repeat is the shorter, uniform sequence TCTGGG. This result suggests mechanistic differences in the action of the telomerases of these closely related yeasts. Despite their length and homogeneity differences, all the Saccharomyces telomeric sequences show a conserved core which is also shared by the Candida glabrata telomeric sequence. This evolutionary similarity may be partly explained by the preservation of a binding site for the RAP1 protein.